From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Jan 30 2009 - 21:21:54 CST
Is is fine if atoms belonging to different segments (having differing
segnames) have identical residue (referred to in VMD as either residue or
resid) numbers.
C.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Fri, Jan 30, 2009 at 1:46 PM, Falgun Shah <fhshah_at_olemiss.edu> wrote: > > Dear NAMD user > > Hi i am using NAMD for MD simulations. My PDB file has 3 segment. When i > added water box the water has been added in 4 segment WT1, WT2, WT3 and WT4. > In addition to it, some residue no. of water molecules are same. Please see > below: > > > ATOM 24426 H1 TIP3W9261 27.288 -18.939 -13.021 1.00 0.00 > WT1 > ATOM 24427 H2 TIP3W9261 27.886 -20.117 -12.282 1.00 0.00 > WT1 > ATOM 24428 OH2 TIP3W 7 -1.947 33.713 -27.286 1.00 0.00 > WT2 > ATOM 24429 H1 TIP3W 7 -1.514 34.539 -27.070 1.00 0.00 > WT2 > ATOM 24430 H2 TIP3W 7 -2.770 33.739 -26.798 1.00 0.00 > WT2 > ATOM 24431 OH2 TIP3W 8 0.779 17.847 17.918 1.00 0.00 > WT2 > > Similar resid no: > > ATOM 19034 OH2 TIP3W*7056* -19.057 19.390 -1.922 1.00 0.00 > WT1 > ATOM 19035 H1 TIP3W7056 -18.887 19.411 -0.980 1.00 0.00 > WT1 > ATOM 19036 H2 TIP3W7056 -18.435 18.748 -2.263 1.00 0.00 WT1 > > ATOM 26291 OH2 TIP3W*7056 * 26.056 -33.151 -1.579 1.00 0.00 > WT2 > ATOM 26292 H1 TIP3W7056 25.973 -32.906 -0.658 1.00 0.00 > WT2 > ATOM 26293 H2 TIP3W7056 27.000 -33.202 -1.729 1.00 0.00 > WT2 > > Do i need to bother about it. > > One more thing! when i did the calculation for RMSD using source rmsd.tcl > > the trajectories look distorted (it was fine when i loaded them). Is it > because of the alignment? but i dont think so. > > Please let me know if it is something unusual. > > Thanks in advance > > -- > Falgun H shah > PhD candidate (3rd year) > Department of Medicinal Chemistry > 2028, Natural Product Center > University of Mississippi > > Ph No: 6629151286(O) > 662 801 5667(M) > email: fhshah_at_olemiss.edu >
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